In the Catalog Setup page there is an option called Order Process. This option controls where your Mals cart will appear. If you choose Inline Frame then the Mals cart will show on your website in an i-frame. This is fine for some applications but can cause problems if the order is too large. To make this work better, go into your Mals account and then to Cart Setup and then to Fonts and Alignment and change the Cart Width and Alignment to say 90% and Centered. You may have to play around with the width depending on your template. 3 column templates will have more problem with this then 2 column.
Another issue with the i-frame setup is that it can setup additional vertical scrollbars within your page and some people might not realize that they are there. This will cause them to not see the Order Buttons and they may get confused and leave your store! So be sure to check this out and do not ignore problems in this area.
The second option here is Normal Window. This setting will send your customers to the Mals site where the cart will be displayed. This is preferable for larger orders and is required if you have an external shipping calculator or you are using the View Cart Contents on your site. You can and should customize this page as much as you can. You can add your logo, change the colors of the header bars and set the text face and size. Try to make this look as much like your site as you can. Be careful using background graphics as they will apply to the entire page and may make the cart hard to read. You should set the Cart Width and Alignment here as well. I like to see the width of the cart equal to your logo, but if you have a small logo then set the width to about 500 ~ 650. I like to see things centered but that is up to you.